I have been particularly keen to list those involving ancient DNA. You will notice right at the top that AMIS is engaged in extracting ancient DNA for several specific projects. By 2014 it hopes to have sequenced the complete mitochondrial genome and Y chromosome of a large sample of Holocene individuals.

You can find the PhD thesis of Marie Lacan on the following link: http://thesesups.ups-tlse.fr/1392 in french. The goal of her project is to study DNA from mediterranean neolithic. In her conclusion, she speak about DNA test on neolithic samples from Italy, Greece, Crete and Cyprius in the future. In a e-mail she sent me at the end of last year, she spoke about DNA test on mediterranean mesolithic.

You can find the PhD thesis of Marie Lacan on the following link: http://thesesups.ups-tlse.fr/1392 in french. The goal of her project is to study DNA from mediterranean neolithic. In her conclusion, she speak about DNA test on neolithic samples from Italy, Greece, Crete and Cyprius in the future. In a e-mail she sent me at the end of last year, she spoke about DNA test on mediterranean mesolithic.

There is a lot more in that thesis that you have read. I’m actually very grateful that you posted the link to it.

Here is Table-1(Pages 48-49) with a description of all the sites analyzed by them, soon to be published:

Table 9 shows that the Mesolithic (dated to 6230-6100 cal. B.C using C14) settlement of Linatzeta, Deba, Guipuzcoa is Haplogrup H, with HVR-I 16309G, and it tested positive for SNPs: H-C7028T having a C in there, and also H-C7028T also having a C in there too.

Table 9 also shows that the late Mesolithic to late Neolithic settlement of Franchthi, Greece is Haplogroup H too, with HVR-I 16293G, and it tested positive for SNPs: H-C7028T having a C in there, and also H-C7028T also having a C in there too.

On the other hand the two samples from Santimamine(Dated to 4000 ybp using C14) tested H1, and U5.

So for all those that were skeptical of the results of Hervella.et.al.2012, now you have it there was indeed mt-DNA H in the FC region pre-Neolithic. It is likely that H and U5 were the two major players in the region.

Also of interest, Page 96 Tables 11 through 13 list the mt-DNA haplogroups and Y-DNA haplogroups of 2 samples from the Dolmen of La Pierre Fritte, France dated using C14 to 2750 to 2725 BC.

So for all those that were skeptical of the results of Hervella.et.al.2012, now you have it there was indeed mt-DNA H in the FC region pre-Neolithic.

Sorry to disappoint you, but no. Unless I misunderstand her French, she is not saying that. She says that she received samples from sites which include burials from the Mesolithic to Neolithic. From each site one sample (no information on date) was used to test for DNA. Two of these yielded a clear result - H in both cases - but without data on who handled the collections, they cannot exclude the possibility of contamination. That alone would rule out publication these days, but also the samples being undated renders them almost useless.

Lacan's much more secure results from the caves of Treilles, France and Avellaner, Spain, were published last year.

Thanks for posting the link to this thesis though secherbernard. Some other additional results are interesting.

Sorry to disappoint you, but no. Unless I misunderstand her French, she is not saying that. She says that she received samples from sites which include burials from the Mesolithic to Neolithic. From each site one sample (no information on date) was used to test for DNA. Two of these yielded a clear result - H in both cases - but without data on who handled the collections, they cannot exclude the possibility of contamination. That alone would rule out publication these days, but also the samples being undated renders them almost useless.

Lacan's much more secure results from the caves of Treilles, France and Avellaner, Spain, were published last year.

No, don’t worry you never disappoint; I know you have an agenda to serve, and you have to hold tight to it, so this wasn’t unexpected. As for the dating issue, here take a look at Table-1:

As you can see, the samples from Cueva de Linatzeta, Deba, Guipuzcoa, which are number 14 in Table-1 have been dated using C14 to 6230 to 6100 BC. So, yeah take a shot at the contamination thing if you want, sooner or later the results would be published, and well, you will have to admit that you were wrong, but it’s OK, we all hold on to our pre-conceived notions, so we’ll see how long before you finally admit the truth.

Here is a Google translate translation of the excerpt I posted:

Quote from: Lacan.et.al.2011

We therefore wanted to confirm the authenticity of these haplotypes by studying the diagnostic positions, localized on the region coding the DNA by mass spectrometry. Of the five samples, only two polymorphisms coherently matched with HVI sequences obtained beforehand: the samples from sites Linatzeta (LTZ-T7) and Franchthi (Fr-63), have enabled to determine the mitochondrial haplogroup individuals . The absence of additional data on these levies, such as DNA of male and female persons in contact with different collections, or other samples containing a different DNA, does not, however, whether the extracted DNA corresponds, for each levy, has endogenous molecules. For the sample of Teviec, analysis of additional positions failed to reinforce the authenticity of the haplotype, or to determine the haplogroup. Finally, for samples Rendina (T5-R) and Los Canes (LC-T9) a book that had yet clear HVI sequence, analysis of diagnostic positions revealed the presence of a mixture of DNA, which polymorphisms characterize several haplogroups, that is to say probably a mixture of molecules belonging to persons different.

Does anyone know what work is currently being done on collecting ancient y-dna?

Should we expect some soon?

What sites are being investigated for y-dna?

Responsible: A. Sevin, M. Gibert

Thirty years ago, aware of the importance of a multidisciplinary approach for studying the Pyrenean population, the CNRS and the Midi-Pyrenees, scientifically and financially supported the Pyrenean Institute of Anthropological Studies (IPEA) and the program CNRS "Anthropology and Ecology Pyrenean" conducted under the supervision of Jean Guilaine. Within the IPEA, the initial biological studies were conducted by the Centre team hémotypologie, who gave birth later in the laboratory of Toulouse Anthropobiology (Lab FRIENDS - ENG No. 2960).

As part of this research, the laboratory became interested in the Pyrenean population dynamics and the impact of geography, economy mode and marriage practices on the structure and population dynamics of the French Pyrenean valleys. The regions studied included the Pays de Sault, the Lavedan, and Larboust Valley Oueil, the Aran Valley and the Upper Valley of the Garonne.

Initial results showed that the relief alone can not explain patterns of population differentiation Pyrenees. Thus, a geographical vision but also demographic and economic space seems necessary to interpret the observed profiles. On this basis we have decided to relaunch a program on "microevolution and population dynamics of the Pyrenees" in our support of the contribution of molecular biology techniques, but also on the growth of knowledge in other disciplines ; especially historical demography and paleoenvironment.

The development of this research is twofold. A first program to enter the Pyrenees as a whole, that is to say, considering the cross-border aspect of population history. This part of the research program is supported by a Working Community of the Pyrenees, to renew relations between the universities of Toulouse (Resp: A. Sevin, Dugoujon JM, Gibert M), Barcelona (Lead MP Aluja, R. Nogues and P. Moral, E. Esteban), Zaragoza (Resp. María Begoña Jarreta, C. Núñez) and Bilbao (Resp. JA Pena), each of these universities have conducted research on the Pyrenean populations.

A second component includes the study of French Pyrenean populations. This includes the study anthropobiologique populations mentioned above, and the study of new populations, including Ariege. The analysis includes 1. The study of genealogy and surname 2. The study of molecular markers. The purpose of genealogical study is firstly to improve the sampling and the definition of (sub) populations, secondly to assess the impact of historical periods on population structure. The analysis of molecular markers provides a second time information about the earliest history of these populations.Among the populations Ariege, special interest was given to the population of the Valley High Vicdessos. This work , done in collaboration with JC Sangoi (Framespa) and N. Telmon (AMIS), is part of the multidisciplinary projects carried by the Observatory gender Male Pyrenees "High Vicdessos" directed by D. Galop (Geode). The possibility of combining the information revealed by different disciplines and will contextualize the history of populations and their interactions with the environment, including in biological terms (collaboration AM Guihard-Costa).

A. Sevin, G. Boëtsch In 1991. Files and genealogical analysis of the genetic structure of populations not isolated. Application to an agricultural population of the Limousin, Cahiers Quebecois Demography, 20: 37-50

Thanks for pointing out the date on the Cueva de Linatzeta specimen. That certainly makes it more interesting, though I can't include it because of the contamination issue.

I have no preconceived notions about mtDNA H. My very first draft of The Peopling of Europe back in March 2009 took seriously the claims of several studies to have found H in Palaeololithic Europe. I was immediately set straight by a wiser person, who pointed out the problem of CRS results in ancient DNA. Still I continued to think that H had spread from Iberia in the Mesolithic until quite recently. The finding of pretty well solid mtDNA haplogroup U, U4 and U5 in Mesolithic central Europe came as a shock to a lot of us I think, but still left room for the idea of H in Mesolithic Iberia. Then a study from Spain attacked that: O. García et al, Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge, Heredity, vol. 106 (2011), pp. 37–45. So I gave up the idea.

Meanwhile estimates of the age of haplogroup H keep falling. The date alone does not rule out the possibility of H in Iberia in 6000 BC. It is just looking more and more likely that it arrived in Europe mainly in the Neolithic.

. . .No, don’t worry you never disappoint; I know you have an agenda to serve, and you have to hold tight to it, so this wasn’t unexpected . . .

Now I am disappointed. It seems a bit unfair to complain about ad hominems and about people insinuating that because you are Basque you have a Basque agenda only to turn around and do the same sort of thing to Jean M.

Thanks for pointing out the date on the Cueva de Linatzeta specimen. That certainly makes it more interesting, though I can't include it because of the contamination issue.

You are welcome. :-) I expect those results to be published soon, so they will address any possible contamination issue, nowadays almost every study in aDNA has to address that issue so, I would imagine whoever did the analysis, also took the precautions.

Meanwhile estimates of the age of haplogroup H keep falling. The date alone does not rule out the possibility of H in Iberia in 6000 BC. It is just looking more and more likely that it arrived mainly in the Neolithic.

I can tell you, that the main problem with the Garcia.et.al.2011 study was that they dumped all the Basques together into the IPNW category. But if one looks at Table-S2 or Table-S1 for example one will find that Vizcayans have 4 mt-DNA lineages of H3, and they have 4 haplotypes for those lineages, so they have a really high haplotype diversity when it comes to H3. So by combining all Basques with Cantabrians, Galicians and other NW Iberians, any possible regional diversity gets obscured.

Now I am disappointed. It seems a bit unfair to complain about ad hominems and about people insinuating that because you are Basque you have a Basque agenda only to turn around and do the same sort of thing to Jean M.

Well, don't be, the issue was a misunderstanding, and hopefully it is cleared now.

For this site, we received three teeth from jaw fragments and / or mandibles found in the ossuary pit-pit which was used according to the latest data C14, at the very end of the Neolithic ( 2800 BC. JC) (Jagu et al. 2008). Again, this was to assess the state of DNA preservation in these biological remains, before considering to make global analyzes of burial.

Of the three samples tested, two have yielded relatively well preserved DNA that allowed us to perform analyzes on mitochondrial DNA, but also on the nuclear DNA. Initially, we sequenced the mitochondrial HVI region, and determined the profile of autosomal individuals to make sure it was not a contaminating DNA, which could have been deposited on the bones during the excavation or anthropological analysis.

Both samples gave different mitochondrial haplotypes, two belonging to haplogroup K (Table 11). Autosomal profiles "consensus" obtained from multiple extractions and amplifications also showed that these were two different individuals, and they were both male. Profiles are still too "partial" in order to highlight possible links of close relatives (Table 12).

Individuals that were male, we also tried to determine the haplotypes Y. We were able to obtain partial haplotypes that appear to be identical on markers amplified. This assumes that the two subjects may belong to the same genetic lineage male. The calculations show that haplotypes shared this haplotype is currently mainly found in Mediterranean populations present (Appendix 3.D). The analysis of the haplotype with the software Haplogroup Predictor suggests, moreover, that the two subjects belong to haplogroup Y I2a1 (Table 13).

The determination of mitochondrial haplogroups and Y from the different haplotypes found, however, must be confirmed and validated by analysis of diagnostic positions before considering conduct additional analysis.

The Neolithic transition has been a major event in the history of the European settlement. To evaluate directly how the neolithization of the Mediterranean basin may have influenced the genome of ancient European individuals, we performed molecular analyses on human remains dated from this period and found in this region.

The analyses focused on 134 samples from 29 different archaeological sites, dating from the Mesolithic to the junction with the protohistoric period. A special attention was paid to two main sites for which the first samples studied appeared to contain relatively well preserved endogenous DNA, the “Cova de l’Avellaner” located in Spanish Catalonia (first half of the fifth millennium BC.) and the “grotte I des Treilles” (Aveyron, France) attributed to the late Neolithic period (about 3000 years BC.).

Despite the difficulties inherent to ancient DNA studies, we were able to analyze several types of molecular markers located on both mitochondrial and nuclear DNA (autosomes and Y chromosome). We obtained new information on the funeral recruitment of the two main cavities (determining the sex of individuals, kinships and the overall genetic structure) and determined the biogeographical origin of the individuals buried. We also analyzed a nuclear polymorphism associated with the lactase persistence.

Basically, the results confirm that the spread of the Neolithic has been a heterogeneous phenomenon in Europe. They also suggest that the impact of this transition has been different on the paternal and maternal genetic lineages. Indeed, if the mitochondrial haplogroups found seem rather stem from the different migration events that populated Europe from the Paleolithic period onwards, most of the Y haplogroups (G2a and E1b1b1a1b) were described to be introduced in Europe with the Neolithic expansion. A bias due to the funeral recruitment, whichtook place in the two sepulchral caves can however explain the low diversity found in the paternal lineages. Further investigations will be necessary to confirm these initial findings. In any case, these results represent, to date, the first data available on the existing paternal lineages at the Neolithic times in the Southwest of Europe.

On the whole, this work demonstrates for the first time, thanks to ancient molecular data that the Neolithic dissemination in south-western Europe has been accompanied by a spread of people along the Mediterranean coasts, which would have introduced new genetic lineages into the Western regions of Mediterranean, from the Balkans and/or the Middle East.

I have printed the thesis of Lacan, and I too thank Bernard for this. I’ll read it as soon as it is possible, in French of course, but the beginning hasn’t been satisfying: no mix between homo sapiens Neanderthalensis and homo sapiens sapiens, what we now know isn’t true, and “three” European Refugia (Cantabrian, Balkan, Ukrainian) and no word about Italy. It seems to me that the writing isn’t updated about this, and probably not only JeanL or Jean Manco may have an agenda.Hope that mademoiselle Lacan were amongst those French who came to Italy to take some ancient bones, like Francesco Mallegni wrote to me. Mademoiselle Lacan will get many surprises.

There is no result about lactose tolerance on Le Dolmen de la Pierre Fritte samples. Marie Lacan gives results about lactose tolerance only on Treilles samples in South France and Avellaner samples in Spain. There is no lactose tolerance for all these samples.

I expect those results to be published soon, so they will address any possible contamination issue, nowadays almost every study in aDNA has to address that issue so, I would imagine whoever did the analysis, also took the precautions.

The problem was not with the analysis, but with the collection of the sample. If an analyst is sent a bit of bone from a museum collection, he or she has no idea who handled the bone when it was taken out of the ground and moved to the museum and so on. These days archaeologists who know that bones may be sampled for DNA etc will wear protective clothing and take other precautions to keep the bone away from possible contamination. Furthermore all those who could have come into contact with the bone during collection and in the laboratory will have their DNA tested to compare with the result from the bone, and rule out contamination.

That is why it is best to take samples from on-going excavations, where these precautions can be taken. That is why the results from Treilles and Avellaner have been published and not the additional results included in Marie Lacan's thesis.

Which should shed some light into the pre- and post- Neolithic haplogroups in Anatolia and the Balkans.

Thanks for posting. I am looking forward to the conclusions of Dan Bradley's project.

"There is a huge wealth of Y chromosome data from modern surveys using a standard reference panel of SNPs that are known to show strong geographical structure. Patterns observed using thousands of samples from Europe and the Near East have been subject to very strong interpretations where, for example the spread of farmers into Europe have been cited as the origin of alternately, i) virtually all, and ii) only a minority of modern European Y chromosome lineages. The postulation of an association between specific SNP lineages and the Near Eastern Neolithic also has led to strong inference about migrations into North Africa at the dawn of agriculture. There is a clear need to produce time-stamped Y chromosome lineages to test and distinguish between these hypotheses.

Simply typing SNPs that have been ascertained using modern sampling gives a risk of missing vital patterns of variants in the past. One cannot assume that all past variants, or even major families of variants from thousands of years ago are represented today; indeed there are indications from other systems that sharp discontinuity from ancient to modern is possible. For this reason we propose to re-sequence the major non-repetitive regions of the Y chromosome in ancient samples. This will cover positions where SNPs have already been ascertained from modern samples, thus embedding these specimens in existing phylogenetic patterns. However, this will also uncover relationships that may be unobtainable from modern study but which may be critical in interpreting relationships among ancient groups.

The ESR of this sub-programme will investigate these anthropological and methodological questions using the DNA libraries generated by the ESR in Mainz, which derive from approximately 200 Mesolithic and Neolithic skeletons from western Anatolia and southeastern Europe. Indexed next generation sequencing libraries will be generated by ligation and PCR. We will use RNA bait capture and Illumina GA next generation sequencing in a range of carefully selected samples to produce ~1 Mb of sequence per individual. The calling of authentic SNPs from ancient material will be non-trivial, given the error rates associated with ancient DNA and NGS. However, methods exist for this and the testing for known SNPs will provide a training data set, allowing a calibration of quality control parameters. Whereas NGS has opened up the prospects of large amounts of data being harvested from ancient samples, the analysis of whole genomes is not yet feasible as a population screening tool. However, the minority of the Y chromosome sequence which is comprised neither of large repeats or simple sequence represents a reasonable target size for the economical screening of multiples samples. The data obtained from this Y-chromosome re-sequencing sub-programme will be compared to modern European Y-chromosome reference data to examine the contribution of these ancient populations to modern European Y-chromosome diversity. These results will be forwarded to the ESRs supervised by Mathias Currat (UNIGE), Mark Thomas (UCL), and Jean-Pierre Bocquet-Appel (CNRS) for incorporation into demographic and genetic models."